Kristina G Hulten1, Robert M Genta2, Ira N Kalfus3, Yi Zhou4, Hongjun Zhang4, David Y Graham5. 1. Department of Pediatrics, Baylor College of Medicine, Houston, Texas. 2. Inform Diagnostics, Irving, Texas; Department of Pathology, Baylor College of Medicine, Houston, Texas. 3. M2G Consulting, New York, New York. 4. American Molecular Laboratories, Vernon Hills, Illinois. 5. Department of Medicine, Michael E. DeBakey VA Medical Center and Baylor College of Medicine, Houston, Texas. Electronic address: dgraham@bcm.edu.
Abstract
BACKGROUND & AIMS: The decline in Helicobacter pylori cure rates emphasizes the need for readily available methods to determine antimicrobial susceptibility. Our aim was to compare targeted next-generation sequencing (NGS) and culture-based H pylori susceptibility testing using clinical isolates and paired formalin-fixed, paraffin-embedded (FFPE) gastric biopsies. METHODS: H pylori isolates and FFPE tissues were tested for susceptibility to amoxicillin, clarithromycin, metronidazole, levofloxacin, tetracycline, and rifabutin using agar dilution and NGS targeted to 23S rRNA, gyrA, 16S rRNA, pbp1, rpoB and rdxA. Agreement was quantified using κ statistics. RESULTS: Paired comparisons included 170 isolates and FFPE tissue for amoxicillin, clarithromycin, metronidazole, and rifabutin and 57 isolates and FFPE tissue for levofloxacin and tetracycline. Agreement between agar dilution and NGS from culture isolates was very good for clarithromycin (κ = 0.90012), good for levofloxacin (κ = 0.78161) and fair for metronidazole (κ = 0.55880), and amoxicillin (κ = 0.21400). Only 1 isolate was resistant to tetracycline (culture) and 1 to rifabutin (NGS). Comparison of NGS from tissue blocks and agar dilution from isolates from the same stomachs demonstrated good accuracy to predict resistance for clarithromycin (94.1%), amoxicillin (95.9%), metronidazole (77%), levofloxacin (87.7%), and tetracycline (98.2%). Lack of resistance precluded comparisons for tetracycline and rifabutin. CONCLUSIONS: Compared with agar dilution, NGS reliably determined resistance to clarithromycin, levofloxacin, rifabutin, and tetracycline from clinical isolates and formalin-fixed gastric tissue. Consistency was fair for metronidazole and amoxicillin. Culture-based testing can predict treatment outcomes with clarithromycin and levofloxacin. Studies are needed to compare the relative ability of both methods to predict treatment outcomes for other antibiotics.
BACKGROUND & AIMS: The decline in Helicobacter pylori cure rates emphasizes the need for readily available methods to determine antimicrobial susceptibility. Our aim was to compare targeted next-generation sequencing (NGS) and culture-based H pylori susceptibility testing using clinical isolates and paired formalin-fixed, paraffin-embedded (FFPE) gastric biopsies. METHODS: H pylori isolates and FFPE tissues were tested for susceptibility to amoxicillin, clarithromycin, metronidazole, levofloxacin, tetracycline, and rifabutin using agar dilution and NGS targeted to 23S rRNA, gyrA, 16S rRNA, pbp1, rpoB and rdxA. Agreement was quantified using κ statistics. RESULTS: Paired comparisons included 170 isolates and FFPE tissue for amoxicillin, clarithromycin, metronidazole, and rifabutin and 57 isolates and FFPE tissue for levofloxacin and tetracycline. Agreement between agar dilution and NGS from culture isolates was very good for clarithromycin (κ = 0.90012), good for levofloxacin (κ = 0.78161) and fair for metronidazole (κ = 0.55880), and amoxicillin (κ = 0.21400). Only 1 isolate was resistant to tetracycline (culture) and 1 to rifabutin (NGS). Comparison of NGS from tissue blocks and agar dilution from isolates from the same stomachs demonstrated good accuracy to predict resistance for clarithromycin (94.1%), amoxicillin (95.9%), metronidazole (77%), levofloxacin (87.7%), and tetracycline (98.2%). Lack of resistance precluded comparisons for tetracycline and rifabutin. CONCLUSIONS: Compared with agar dilution, NGS reliably determined resistance to clarithromycin, levofloxacin, rifabutin, and tetracycline from clinical isolates and formalin-fixed gastric tissue. Consistency was fair for metronidazole and amoxicillin. Culture-based testing can predict treatment outcomes with clarithromycin and levofloxacin. Studies are needed to compare the relative ability of both methods to predict treatment outcomes for other antibiotics.
Authors: David Y Graham; Yamil Canaan; James Maher; Gregory Wiener; Kristina G Hulten; Ira N Kalfus Journal: Ann Intern Med Date: 2020-05-05 Impact factor: 25.391
Authors: Olga P Nyssen; Dmitry Bordin; Bojan Tepes; Ángeles Pérez-Aisa; Dino Vaira; Maria Caldas; Luis Bujanda; Manuel Castro-Fernandez; Frode Lerang; Marcis Leja; Luís Rodrigo; Theodore Rokkas; Limas Kupcinskas; Jorge Pérez-Lasala; Laimas Jonaitis; Oleg Shvets; Antonio Gasbarrini; Halis Simsek; Anthony T R Axon; György Buzás; Jose Carlos Machado; Yaron Niv; Lyudmila Boyanova; Adrian Goldis; Vincent Lamy; Ante Tonkic; Krzysztof Przytulski; Christoph Beglinger; Marino Venerito; Peter Bytzer; Lisette Capelle; Tomica Milosavljević; Vladimir Milivojevic; Lea Veijola; Javier Molina-Infante; Liudmila Vologzhanina; Galina Fadeenko; Ines Ariño; Giulia Fiorini; Ana Garre; Jesús Garrido; Cristina F Pérez; Ignasi Puig; Frederic Heluwaert; Francis Megraud; Colm O'Morain; Javier P Gisbert Journal: Gut Date: 2020-09-21 Impact factor: 23.059
Authors: Monique M Gerrits; Marco Berning; Arnoud H M Van Vliet; Ernst J Kuipers; Johannes G Kusters Journal: Antimicrob Agents Chemother Date: 2003-09 Impact factor: 5.191
Authors: Monique M Gerrits; Marcel R de Zoete; Niek L A Arents; Ernst J Kuipers; Johannes G Kusters Journal: Antimicrob Agents Chemother Date: 2002-09 Impact factor: 5.191